.git/hooks folder missing when running CI job

I just migrate from gitlab 8.15.x (docker version) to 8.16.3 (omni). And all CI job failed.

It shows

Running with gitlab-ci-multi-runner 1.10.3 (ba2bc36)
Using Docker executor with image python:3.5 ...
Starting service mysql:5.7 ...
Pulling docker image mysql:5.7 ...
Starting service redis:2.8 ...
Pulling docker image redis:2.8 ...
Starting service mongo:3.2 ...
Pulling docker image mongo:3.2 ...
Starting service hedenstroem/elasticsearch:latest ...
Pulling docker image hedenstroem/elasticsearch:latest ...
Waiting for services to be up and running...
Pulling docker image python:3.5 ...
Running on runner-a1c98b2d-project-1661-concurrent-0 via ip-10-0-1-129...
Cloning repository...
Cloning into '/builds/zhouxiaofeng/comments'...
Checking out 65c194c1 as 17-add-searching-tags-by-es...
Skipping Git submodules setup
$ make pip
make[1]: Entering directory '/builds/xxx/comments'
cp: cannot create regular file ‘.git/hooks/’: Not a directory
make[1]: *** [pre-commit] Error 1
Makefile:19: recipe for target 'pre-commit' failed
make[1]: Leaving directory '/builds/xxx/comments'
Makefile:25: recipe for target 'pip' failed
make: *** [pip] Error 2
ERROR: Build failed: exit code 1

And when I try to list all files in the CI job, there is no .git/hooks folder at all.

That’s really weird. Could anyone help me?